[gmx-users] Spatial distribution

Gadzikano Munyuki Gadzikano.Munyuki at uct.ac.za
Sat Nov 8 16:54:29 CET 2008

HI Chris 

I followed the steps below and when i tried to run g_spatial it executed g_cluster instead. Even when i do g_spatial -h it looks like its being overwritten by g_cluster

1.I  used make_ndx to create a group containing the atoms around which i  want
the SDF
2. trjconv -s md.tpr -f tyrc_md.trr -o tyrc1.xtc -center tric -ur compact -pbc  none
3. trjconv -s md.tpr -f tyrc1.xtc -o  tyrc2.xtc -fit rot+trans
4.  g_spatial -s md.tpr -f tyrc2.xtc -n index.ndx

I wrote g_spatial and it should produce a spatial distribution  
function. However, it's rather complicated to use. Did you follow the  
directions in g_spatial -h ? There are about 10 steps to use it. It is  
so complicated on purpose in order to give the user full flexibility,  
but this means that you need to do all of your alignment yourself. If  
you did that correctly, then I also suggest that you should make sure  
that you are visualizing it correctly in VMD. By default you will see  
some atoms, but that is only there because VMD will not recognize a  
gaussian cube without any atoms, and also it makes it easier for you  
to ensure that any other pdbs you may load overlay correctly.  
Therefore ensure that you switch the representation to isosurface and  
then slide the bar so that you see the appropriate isosurface contour.

Please report back to the list with findings so that other users can  
later benifit from your work


Gadzikano Munyuki wrote:
> I want to analyse the solvent around a peptide . I used g_sdf and  
> the output  that i am getting (i.e the refmol.gro) does not have the  
> whole peptide molecule but just the residues that i use to define  
> the coordinate system . I then tried to use g_spatialbut its doing  
> something very different and not spatial distibution, it looks like   
> its executing g_cluster instead. I was wondering if g_custer and  
> g_spatial are meant to do the same thing.

Have a read of g_cluster -h and g_spatial -h and decide whether they're
doing the same thing :-)




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